crash on multiple queries to postgresql db

Dylan Beaudette wrote:

Subsequent calls to:

conn <- dbConnect(PgSQL(), host="localhost", dbname="xxx", user="xxx")
query <- dbSendQuery(conn, query_text)
res <- dbGetResult(query)

are resulting in this:

*** glibc detected *** /usr/local/lib/R/bin/exec/R: realloc(): invalid

other attached packages:
[1] RdbiPgSQL_1.8.0 Rdbi_1.8.0      lattice_0.17-20

Any ideas?

Well, first off, since you are apparently using RdbiPgSQL from
bioconductor, you should probably try asking there.

But in any case, you might try the latest release from bioconductor:
http://www.bioconductor.org/packages/release/bioc/src/contrib/RdbiPgSQL_1.1
6.0.tar.gz

or else try the recently released PostgreSQL DBI package on CRAN:
http://cran.stat.ucla.edu/src/contrib/RPostgreSQL_0.1-3.tar.gz

HTH,

Joe

Thanks Joe. I have updated all of my R packages, along with my Bioconductor 
packages... and I still get the odd behavior:

*** glibc detected *** /usr/local/lib/R/bin/exec/R: realloc(): invalid old 
size: 0xb7dad1e0 ***
======= Backtrace: =========
/lib/i686/cmov/libc.so.6[0xb7cc3624]
/lib/i686/cmov/libc.so.6[0xb7cc71a1]
/lib/i686/cmov/libc.so.6(realloc+0x106)[0xb7cc7b46]
/usr/local/pgsql/lib/libpq.so.5[0xb7802166]
/usr/local/pgsql/lib/libpq.so.5[0xb780239c]
/usr/local/pgsql/lib/libpq.so.5[0xb77fbd31]
/usr/local/pgsql/lib/libpq.so.5(PQfinish+0x15)[0xb77fbe85]
/usr/local/lib/R/site-library/RdbiPgSQL/libs/RdbiPgSQL.so(PgSQLcloseConnection+0x38)
[0xb783bb98]

Again, here is my session info:

R version 2.8.0 (2008-10-20) 
i686-pc-linux-gnu 

locale:
LC_CTYPE=en_US.UTF-8;LC_NUMERIC=C;LC_TIME=en_US.UTF-8;LC_COLLATE=en_US.UTF-8;LC_MONETARY=C;LC_MESSAGES=en_US.UTF-8;LC_PAPER=en_US.UTF-8;LC_NAME=C;LC_ADDRESS=C;LC_TELEPHONE=C;LC_MEASUREMENT=en_US.UTF-8;LC_IDENTIFICATION=C

attached base packages:
[1] grid      stats     graphics  grDevices utils     datasets  methods  
[8] base     

other attached packages:
[1] RdbiPgSQL_1.16.0 Rdbi_1.16.0      lattice_0.17-20


Here is the code that appears to be causing the problems:

# load data from a PostGreSQL database, and return a dataframe
# this will get called whenever the parent function is called
# crashes after 3-5 subsequent calls
load_sensor_data <- function(query_text)
{

# conn becomes an object which contains the DB connection:
conn <- dbConnect(PgSQL(), host="localhost", dbname="SJER", user="dylan")

## pre-filter out possible bad data:
query <- dbSendQuery(conn, query_text)

# fetch data according to query:
res <- dbGetResult(query) 

# convert characters to factors
res <- transform(res, probe_id = factor(probe_id))
res <- transform(res, pedon_id = factor(pedon_id))

# generate a new date-time object in the dataframe
res$date <- as.POSIXct(strptime(res$date_time, format="%a %b %e %H:%M:%S %Y"))

# cleanup
dbDisconnect(conn)

# doesn't completely fix problem crashing
gc()

# return the resulting dataframe
return(res)
}


Thanks in advance,

Dylan

Dylan Beaudette
Soil Resource Laboratory
http://casoilresource.lawr.ucdavis.edu/
University of California at Davis
530.754.7341